In this study we determined the complete nucleotide sequences of the mitochondrial DNA of the ranid frog Rana nigromaculata and the rhacophorid frog Buergeria buergeri. The gene content, nucleotide composition, and colon usage of these frogs conformed to those of typical vertebrate patterns. However, due to an accumulation of lengthy repetitive sequences into the D-loop region, these species possess the large mitochondrial genomes among all the vertebrates examined so far (Rana nigromaculata, 17,804 bp ; Buergeria buergeri, 19,959 bp). In a comparison of gene organizations among amphibian species (Xenopus, salamanders and a caecilian), the positioning of four tRNA genes and the ND5 gene in the mtDNA of B. buergeri diverged from the common vertebrate gene arrangement shared in Xenopus, salamander and caecilian. The unique positions of the tRNA genes in B. buergeri are shared by ranid frogs, indicating that the rearrangements of the tRNA genes occurred in a common ancestral lineage of ranids and rhacophorids. On the other hand, the novel position of the ND5 gene seemed to have arisen in a lineage leading to rhacophorids (and other closely related taxa) after ranid divergence. Phylogenetic analysis based on nucleotide sequence data of all mitochondrial genes also supported the gene rearrangement pathway